{"title":"The VEGA web service: multipurpose online tools for molecular modelling and docking analyses.","authors":"Alessandro Pedretti, Serena Vittorio, Emanuela Sabato, Giulio Vistoli, Angelica Mazzolari","doi":"10.1002/minf.202300018","DOIUrl":null,"url":null,"abstract":"<p><p>The paper presents the VEGA Online web service, which includes a set of freely available tools deriving from the development of the VEGA suite of programs. In detail, the paper is focused on two tools: the VEGA Web Edition (WE) and the Score tool. The former is a versatile file format converter including relevant features for 2D/3D conversion, for surface mapping and for editing/preparing input files. The Score application allows rescoring docking poses and in particular includes the MLP Interactions Scores (MLPInS) for describing hydrophobic interactions. To the best of our knowledge, this web service is the only available resource by which one can calculate both the virtual log P of a given input molecule according to the MLP approach plus the corresponding MLP surface.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":null,"pages":null},"PeriodicalIF":2.8000,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Informatics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1002/minf.202300018","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0
Abstract
The paper presents the VEGA Online web service, which includes a set of freely available tools deriving from the development of the VEGA suite of programs. In detail, the paper is focused on two tools: the VEGA Web Edition (WE) and the Score tool. The former is a versatile file format converter including relevant features for 2D/3D conversion, for surface mapping and for editing/preparing input files. The Score application allows rescoring docking poses and in particular includes the MLP Interactions Scores (MLPInS) for describing hydrophobic interactions. To the best of our knowledge, this web service is the only available resource by which one can calculate both the virtual log P of a given input molecule according to the MLP approach plus the corresponding MLP surface.
本文介绍了VEGA在线web服务，其中包括一套源自VEGA程序套件开发的免费工具。具体来说，本文重点介绍了两个工具:VEGA Web Edition (WE)和Score工具。前者是一个通用的文件格式转换器，包括2D/3D转换、表面映射和编辑/准备输入文件的相关功能。Score应用程序允许对对接姿势进行评分，特别是包括MLP相互作用分数(mlpin)，用于描述疏水相互作用。据我们所知，这个web服务是唯一可用的资源，通过它可以根据MLP方法和相应的MLP表面计算给定输入分子的虚拟log P。
期刊介绍：
Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010.
Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation.
The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.
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